2CWO | pdb_00002cwo

Crystal structure of RNA silencing suppressor p21 from Beet Yellows Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.244 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2CWO

This is version 1.3 of the entry. See complete history

Literature

RNA Silencing Suppressor p21 of Beet Yellows Virus Forms an RNA Binding Octameric Ring Structure

Ye, K.Patel, D.J.

(2005) Structure 13: 1375-1384

  • DOI: https://doi.org/10.1016/j.str.2005.06.017
  • Primary Citation Related Structures: 
    2CWO

  • PubMed Abstract: 

    Many plant viruses encode proteins that suppress the antiviral RNA silencing response mounted by the host. The suppressors p19 from tombusvirus and p21 from Beet yellows virus appear to block silencing by directly binding siRNA, a critical mediator in the process. Here, we report the crystal structure of p21, which reveals an octameric ring architecture with a large central cavity of approximately 90 A diameter. The all alpha-helical p21 monomer consists of N- and C-terminal domains that associate with their neighboring counterparts through symmetric head-to-head and tail-to-tail interactions. A putative RNA binding surface is identified in the conserved, positive-charged inner surface of the ring. In contrast to the specific p19-siRNA duplex interaction, p21 is a general nucleic acid binding protein, interacting with 21 nt or longer single- and double-stranded RNAs in vitro. This study reveals an RNA binding structure adopted by the p21 silencing suppressor.


  • Organizational Affiliation
    • Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 91.04 kDa 
  • Atom Count: 5,388 
  • Modeled Residue Count: 660 
  • Deposited Residue Count: 788 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA silencing suppressor
A, B, C, D
197Beet yellows virusMutation(s): 0 
Gene Names: p21
UniProt
Find proteins for Q08545 (Beet yellows virus (isolate Ukraine))
Explore Q08545 
Go to UniProtKB:  Q08545
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08545
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.244 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.633α = 90
b = 199.633β = 90
c = 56.122γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Refinement description